1. science
2. biology
3. molecular biology

 Genome Science
Biology, Technology & Bioinformatics Department of Zoology & Lady Margaret Hall, Oxford 1st-­‐3rd September 2014 www.genomescience.org.uk #ukgs2014 Day 1: Monday 1st September 2014 Registration: 1.00pm – 6.45pm Department of Zoology Check-­‐in: 1.00pm – 3.00pm Lady Margaret Hall Satellite Workshop: Cloud Infrastructure for Microbial Genomics (CLIMB) The Medical Research Council has recently awarded £8.4m to the CLIMB consortium to support microbial genome bioinformatics and training. The consortium, comprised of Warwick, Birmingham, Cardiff and Swansea, is investing in computer hardware and storage infrastructure in order to provision the world's largest computing 'cloud' dedicated to UK academics engaged in microbial genomics research. This investment will be supported by a busy programme of training activities. Join us before the UK Genome Science meeting officially commences to find out more about what is planned, and help us shape the direction of the project. Time: Monday 1st September 2014 11.30am – 1.15pm Location: Lecture theatre B Chair: Nick Loman (University of Birmingham) 11.30—11.35 Nick Loman Chair's introduction University of Birmingham 11.35—12.00 Sam Sheppard Introduction to the CLIMB project University of Swansea 12.00—12.30 Tom Connor Microbial bioinformatics in the University of Cardiff cloud 12.30—13.00 Daniel Falush Campylobacter genomics Max Planck Institute 13.00—13.15 Discussion Session 1: Opening Remarks & Keynote Lecture Time: Monday 1st September 2014 3.00pm-­‐4.00pm Location: Lecture theatre A Chair: Chris Ponting (MRC FGU & CGAT, University of Oxford) 15.00—15.15 Chris Ponting Opening remarks MRC FGU & CGAT, Oxford 15.15—16.00 Jackie Hunter From genome to phenome – the BBSRC promise of big data Jackie Hunter, Chief Executive of the BBSRC Professor Jackie Hunter joined the BBSRC as Chief Executive in October 2013. Jackie has over thirty years of experience in the bioscience research sector, working across academia and industry and playing a key role in innovative collaborations and partnerships. She holds a personal chair from St George’s Hospital Medical School, which was awarded in recognition of her contribution to bioscience research. Jackie Hunter gained her first degree in Physiology and Psychology at the University of London followed by her PhD which was carried out at the Zoological Society of London. She undertook a Wellcome Trust post-­‐doctoral research fellowship at St George’s Hospital Medical School before taking a role in the pharmaceutical sector in 1983. During her career in industry, as well as leading neurology and gastrointestinal drug discovery and development, Jackie also spent several years developing and leading GSK's external science engagement strategy. In this role she played a central part in fostering effective and innovative collaborations and partnerships between university and institute research groups and the company. From 2004, Jackie was a member of BBSRC Council and BBSRC Strategy Board. She is a fellow of the British Pharmacological Society. She founded OI Pharma Partners in 2010 to support the life science sector in harnessing the power of open innovation. Open innovation allows public and private organisations to use a range of collaborative models to find the best ways to bring ideas to fruition. Jackie was awarded a CBE in the Queen's Birthday Honours list for Services to the Pharmaceutical Industry as well as the Women of Achievement in Science, Engineering and Technology (SET) awards in the category SET Discovery, Innovation and Entrepreneurship in 2010. Parallel session 2a: Emerging Technologies Time: Monday 1st September 2014 4.05pm-­‐6.45pm Location: Lecture theatre A Chair: Mike Quail (Wellcome Trust Sanger Institute) 16.05—16.35 Clive Brown Methods and devices for DNA/RNA Oxford Nanopore sequencing using nanopores 16.35—17.05 Chas André Single-­‐molecule DNA analysis with PicoSeq SIMDEQ 17.05—17.45 Coffee break 17.45—18.15 Iain Macaulay G&T-­‐Seq: Combined DNA and RNA WTSI sequencing from a single cell 18.15—18.30 Cameron Frayling Base4’s microdroplet sequencing Base4 technology: a first look 18.30—18.45 Gabriele Migliorini Capture Hi-­‐C (cHi-­‐C) identifies the ICR chromatin interactome of colorectal cancer risk loci Wine Reception & Poster Session 1 (odd numbers): 6.45-­‐8.30pm (Zoology) Parallel session 2b: Genome Evolution Time: Monday 1st September 2014 4.05pm-­‐6.45pm Location: Lecture theatre B Chair: Chris Ponting (MRC FGU & CGAT, University of Oxford) 16.05—16.35 Judith Mank The evolution of sexual dimorphism: UCL Linking intra-­‐sexual phenotypic and transcriptional variation across the genome 16.35—17.05 Aziz Aboobaker Understanding the biology of pluripotent Zoology, Oxford stem cells from flatworms 17.05—17.45 Coffee break Seeking lncRNA function through 17.45—18.15 Chris Ponting MRC FGU & CGAT, experimental and computational genomics Oxford 18.15—18.30 Christoph Hahn Efficient recovery of complete organelle University of Hull genomes and nuclear genes from genomic NGS data by baiting and iterative mapping 18.30—18.45 Amir Szitenberg The phylogenetic effect on the University of Hull abundance of transposable elements in Nematoda Wine Reception & Poster Session 1 (odd numbers): 6.45-­‐8.30pm (Zoology) Day 2: Tuesday 2nd September 2014 Parallel session 3a: Big Data Analysis Time: Tuesday 2nd September 2014 9.00am-­‐12.45pm Location: Lecture theatre A Chair: Chris Yau (Wellcome Trust Centre for Human Genetics, University of Oxford) 9.00—9.30 Chris Yau Quantifying the true extent of WTCHG, Oxford heterogeneity in the cancer genome: advanced computational methods for characterising uncertainty in tumour heterogeneity deconvolution 9.30—10.00 Oliver Stegle Modeling gene expression heterogeneity EBI between individuals and single cells 10.00—10.30 Jean-­‐Phillipe Vert Reconstructing the 3D architecture of the Institut Curie genome 10.30—11.15 Coffee break 11.15—11.45 Caleb Webber Disease, networks and epistasis MRC FGU, Oxford 11.45—12.15 Julian Knight From genetic association to function: WTCHG, Oxford insights from genomic mapping of regulatory variants in immune disease phenotypes 12.15—12.45 Magnus Rattray Bayesian non-­‐parametric methods for University of modelling transcription and its regulation Manchester Lunch & Poster Session 2 (even numbers): 12.45pm-­‐2.30pm Parallel session 3b: Environmental Genomics Time: Tuesday 2nd September 2014 9.00am-­‐10.30am Location: Lecture theatre B Chair: Peter Kille (University of Cardiff) & Dawn Field (CEH, Wallingford) 9.00—9.30 Dawn Field CEH, Wallingford 9.30—10.00 Mark Blaxter University of Edinburgh Sequencing the Earth: Genomic Observatories and Ocean Sampling Day Wolbachia in nematodes: unexpected associations and palaeosymbiology Towards understanding the functional and taxonomic repertoire of microbial communities using the EBI metagenomics portal 10.00—10.30 Rob Finn EBI Coffee break: 10.30am-­‐11.15am Parallel session 3c: Proffered Abstracts Time: Tuesday 2nd September 2014 11.15am-­‐12.45pm Location: Lecture theatre B 11.15—11.45 Krzysztof Poterlowicz University of Bradford 11.45—12.15 Daniel Wong WTCHG, Oxford 12.15—12.45 Stephen Sansom Kennedy Institute, Oxford Probabilistic modelling of 5C and ChIP-­‐
Seq profiles reveal a high-­‐resolution spatial genomic proximity network controlling epidermal keratinocyte differentiation Epigenomic profiling of the MHC transactivator CIITA using an integrated ChIP-­‐seq and genetical genomics approach Population & single cell transcriptomics reveal the Aire-­‐
dependency, composition and relief from Polycomb silencing of self-­‐
antigen expression in thymic epithelia Lunch & Poster Session 2 (even numbers): 12.45pm-­‐2.30pm Parallel session 4a: Bioinformatics Infrastructure Time: Tuesday 2nd September 2014 2.30pm-­‐5.45pm Location: Lecture theatre A Chair: Mick Watson (The Roslin Institute, University of Edinburgh) 14.30—15.00 Niklas Blomberg The ELIXIR bioinformatics ELIXIR infrastructure: Data, Computing and Services to Communities 15.00—15.30 Michael Eberle Building a Better Medical Illumina Genome 15.30—16.00 Geraldine Van der Auwera Analyzing large cohorts without Broad Institute losing your mind: GATK's new reference model pipeline for variant discovery 16.00—16.45 Coffee break 16.45—17.15 Matthew Addis Maintaining the long-­‐term value Arkivum of NGS data 17.15—17.45 Marghoob Mohiyuddin Addressing the most challenging Bina Technologies variant calling in next generation sequencing and assessing its performance Parallel session 4b: Plant Genomics Time: Tuesday 2nd September 2014 2.30pm-­‐5.45pm Location: Lecture theatre B Chair: Neil Hall (University of Liverpool) 14.30—15.00 Anthony Hall Mutant hunting in complex University of Liverpool genomes 15.00—15.30 Richard Buggs Can genomics help forestry? QMUL The potato genome: Marker 15.30—16.00 Glenn Byran discovery, diversity studies and The James Hutton Institute trait analysis 16.00—16.45 Coffee break 16.45—17.15 Steven Kelly Dissecting the regulatory University of Oxford network governing C4 photosynthesis through exploitation of natural variation Back to BACs? A High-­‐
17.15—17.45 Darren Heavens Throughput, low cost BAC TGAC sequencing pipeline Session 5: Keynote lecture Time: Tuesday 2nd September 2014 5.45pm-­‐6.30pm Location: Lecture theatre A Chair: Rory Bowden (WTCHG, University of Oxford) 17.45—18.30 George Weinstock The Jackson Laboratory Genomic studies of the human microbiome and disease George Weinstock, The Jackson Laboratory Prof. Weinstock applies high-­‐throughput DNA sequencing, genome-­‐wide analysis, bioinformatics, and other genetic methods to the study of human, model organisms and microbial genomes. His goal is to employ genetic and genomic thinking to important problems in biology. He led one of the first bacterial genome projects, sequencing Treponema pallidum, the causative agent of syphilis. He is now a leader of the Human Microbiome Project, studying the collection of microbes that colonize the human body. The goal of this work is to analyze the genomes of these organisms, characterize the communities they form, and measure how communities change in different health and disease states. He was one of the leaders of the Human Genome Project and also the first personal genome project, sequencing Dr. James Watson’s genome using next-­‐generation sequencing technology. He is now leading projects using next-­‐generation sequencing to discover mutations causing human disease. George Weinstock has recently joined the research faculty of The Jackson Laboratory for Genomic Medicine in Farmington, Connecticut. Previously, he was Professor of Genetics and Professor of Molecular Microbiology at Washington University. Prof Weinstock was also Co-­‐Director of the Human Genome Sequencing Center at Baylor College of Medicine in Houston, Texas and Professor of Molecular and Human Genetics there. Dr. Weinstock received his B.S. degree from the University of Michigan (Biophysics, 1970) and his Ph.D. from the Massachusetts Institute of Technology (Microbiology, 1977). Conference Dinner Time: Tuesday 2nd September 2014 7.30pm-­‐11.00pm Location: Lady Margaret Hall Day 3: Wednesday 3rd September 2014 Session 6: Sponsors Session Time: Wednesday 3nd September 2014 9.00-­‐10.30am Location: Lecture theatre A Chair: David Buck (Oxford Genomics Centre, WTCHG, University of Oxford) 9.00—9.20 Scott Brouilette Accelerating the validation of Illumina genomic variants with CRISPR/Cas9 genome editing 9.20—9.40 Mike Lelivelt Ion Torrent semiconductor Life Technologies sequencing update 9.40—10.00 Sudipto Das Tailoring approaches for whole Roche exome & epigenome analysis from a FFPE sample perspective 10.00—10.10 Berwyn Lloyd Automated solutions for NGS Beckman Coulter sample preparation 10.10—10.20 Paul Butler Automation of NGS sample Perkin Elmer preparation: from benchtop NGS to genome centres 10.20—10.30 Dalia Daujotyte RNA-­‐Seq sample prep does not Lexogen need to be complicated Coffee break: 10.30-­‐11.15am Parallel session 7a: Clinical Genomics Time: Wednesday 3nd September 2014 11.15am-­‐3.15pm Location: Lecture theatre A Chair: Nazneen Rahman (Institute of Cancer Research) 11.15—11.45 Nazneen Rahman Implementing genomic medicine – ICR cancer predisposition as an exemplar 11.45—12.15 Ultan McDermott Personalised cancer medicine in the WTSI era of genome sequencing 12.15—12.45 Sian Ellard Genomic testing leads clinical care in University of Exeter neonatal diabetes: a new paradigm 12.45—14.00 Lunch 14.00—14.30 Mark Pallen Clinical microbial genomics and University of Warwick metagenomics: overview and applications Accurate and high resolution HLA 14.30—14.45 Hang Phan typing from targeted exome WTCHG, Oxford sequencing data 14.45—15.00 Susanne Weller “From bench to bedside” via University of Oxford bioinformatics: Advances in cancer research and diagnostics 15.00—15.15 Organisers Closing remarks Close: 3.15pm Parallel session 7b: Microbial Genomics Time: Wednesday 3nd September 2014 11.15am-­‐3.15pm Location: Lecture theatre B Chair: Nick Loman (University of Birmingham) 11.15—11.45 Nick Loman Nanopore sequencing in clinical University of Birmingham microbiology 11.45—12.15 Zam Iqbal Translation of sequencing from WTCHG, Oxford research to the clinic: an example 12.15—12.45 Holly Bik The genome deficit for microbial UC Davis eukaryotes 12.45—14.00 Lunch 14.00—14.30 Torsten Seemann Rapid bacterial outbreak Monash, Melbourne characterization from high-­‐
throughput sequencing data 14.30—14.45 Camilla Ip A pipeline for inferring the diversity WTCHG, Oxford of intra-­‐host quasi-­‐species of Hepatitis C virus genomes sequenced with a new probe-­‐
capture viral RNA-­‐Seq protocol 14.45—15.00 Sebastian van Hal Molecular epidemiology of University of Western Vancomycin Resistance Sydney Enterococcus faecium bactereamia 15.00—15.15 Organisers Closing remarks Close: 3.15pm Department of Zoology Tinbergen Building, South Parks Road, OX1 3PS Visitor Health and Safety Information Welcome to the Department of Zoology, Tinbergen Building. This leaflet provides you with essential safety information you should read and understand in the unlikely event of any emergency situation arising during your stay. Emergency Contact Numbers Fire, Ambulance, Police -­‐ Tel: 999 University Security Services -­‐ Tel: (2) 89999 Zoology Reception -­‐ Tel: (2) 71234 In the event of discovering a fire Your host will make you aware of your nearest fire exits at the start of your stay. Please make sure you understand their instructions. If you discover a fire, raise the alarm by breaking the glass in any of the red ‘FIRE’ call points and leave the building via the nearest exit. Please report to outside reception to provide the response team with information on the fire. In the event of the fire alarm sounding -­‐ Leave the building via the nearest exit and proceed to the assembly point on the Mansfield Road playing fields (see Fig 1) -­‐ Do not stop to collect personal belongings -­‐ Close all doors behind you -­‐ Do not use the lifts -­‐ Do not re-­‐enter the building until authorised to do so Alarm Testing The fire alarm is sounded every Tuesday at 10am for a few seconds. In the event of this alarm not stopping please treat as a real emergency and leave the building. Mobility – Evacuation Assistance If you require assistance in the event of a building evacuation please go to one of the refuge points located on levels A, C, D and E. From here call reception using the red emergency phones. If required, trained staff can evacuate persons using the EVAC chairs. Anyone unable to use the stairways should avoid the use of level F. Assembly Point – Mansfield Road Playing Fields LTA = Lecture Theatre A (Level B) R LTC LTA LTB LTB = Lecture Theatre B (Level A) LTC = Lecture Theatre C (Level A) R = Reception Fig 1: Evacuation routes shown are for illustration only to show the general direction of travel. Please follow the green exit signs. Your host will explain your nearest fire exit and evacuation route. First Aid The Department has a team of trained first aiders. If you feel unwell or are injured please report to reception (Tel: (2) 71234) who will organise first aid assistance. Out of hours first aid assistance is available from the University Security Services – Tel: (2) 89999 Accidents & Incidents Please report all accidents and incidents within the department to reception (Tel: (2) 71234) who will contact the Safety Officer. Premium Sponsors Additional Sponsors